Hello friends I am new to the RNA-seq anaIyse have fastq files single end (1x50) of mRNA and sRNA (each file contains the reads of two organisms) ad and I want to study the expression of genes in each sample.
I made a mapping by STAR for the first sample train with the following command:
$ Linux_x86_64/STAR --runThreadN 12 --genomeDir /index --sjdbOverhang 49 --readFilesIn /sample1.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix /output -outSAMtype BAM SortedByCoordinate
but I got :
Uniquely mapped reads% | 58.83% % of reads mapped to multiple loci | 38.77% % of reads mapped to too many loci | 0.46%
I do not understand why I got this high percentage of reads mapped to multiple loci. Do you have an idea to improve the result of the mapping of mRNA in the STAR command that I used ???????
What is the best way to map sRNA reads to the reference genome ??
Thank you in advance